The alert was issued around 4:30pm Thursday after someone claimed to have spotted a man carrying a wooden-handled handgun near the University Center Garage.
The alert directed those in campus buildings to remain where they were and those outdoors to seek shelter. Then just before 5:30 p.m., the school's website said those on campus could "resume activities" but remain cautious.
School spokesman Jason Cook said someone on campus made the report, and police were searching the central part of the 5,000-acre university.
"At this point we have not been able to confirm that report," Cook said.
The alert said a caller reported seeing a man carrying a wood-handled handgun heading toward the university's Sanders Corps Center. The suspect was described as a mid-to-late 40s white male, about 5 feet 5 inches tall with a skinny build, with light-colored hair and wearing a lime-green short-sleeved button-up shirt and jeans.
The university says an investigation is ongoing.
Code Maroon is Texas A&M University's emergency notification system.
The Associated Press contributed to this report.